vgteam/long-read-giraffe-experiments issues and pull requests

#68 - Add sniffles

Pull Request - State: closed - Opened by xchang1 24 days ago

#67 - Chunked graphaligner

Pull Request - State: closed - Opened by xchang1 24 days ago

#66 - Set up shared SnakeMake output location that Adam and Xian can both run against

Issue - State: closed - Opened by adamnovak 3 months ago - 1 comment

#65 - Merge DV WDL changes back to Snakemake

Issue - State: closed - Opened by adamnovak 3 months ago - 3 comments

#64 - Attach SV calling to Snakemake?

Issue - State: closed - Opened by adamnovak 3 months ago

#63 - Add multiple minimap2 presets (lr:hq and tech-named one)

Issue - State: closed - Opened by adamnovak 3 months ago - 1 comment

#62 - Add haplotype sampling to Snakemake

Issue - State: closed - Opened by adamnovak 3 months ago - 1 comment

#61 - Add a target to make the One True List of Files to the Snakemake, along with experiment configs for it

Issue - State: closed - Opened by adamnovak 3 months ago

#60 - Evaluate DV calling on HG001 AKA NA12878 using its new assembly-based benchmark

Issue - State: open - Opened by adamnovak 3 months ago - 2 comments

#59 - Summary Statistics Table

Issue - State: open - Opened by adamnovak 3 months ago

#58 - Investigate low SV calling accuracy on the unfiltered graph

Issue - State: open - Opened by adamnovak 3 months ago

#57 - Test DV calling against the HPRC Release 2 provisional graphs with the WDL

Issue - State: closed - Opened by adamnovak 3 months ago - 1 comment

#56 - Fix weirdly low DV accuracy on the unfiltered HPRC graphs

Issue - State: closed - Opened by adamnovak 4 months ago

#55 - Fix very high false negative rate for insertion SVs with LRG

Issue - State: open - Opened by adamnovak 4 months ago - 1 comment

#54 - Collect speed results, sim accuracy results, and real calling results for Giraffe all together

Issue - State: open - Opened by adamnovak 5 months ago

#53 - Evaluate HiFi DV accuracy after training

Issue - State: closed - Opened by adamnovak 5 months ago

#52 - Stop tracking provenance specifically when measuring speed

Issue - State: closed - Opened by adamnovak 6 months ago

#51 - Investigate if graph alignments of nanopore reads that get long softclips at surjection are correct

Issue - State: open - Opened by adamnovak 7 months ago - 2 comments

#50 - Upgrade to HPRC Year1-3 data and Release 2 graphs

Issue - State: closed - Opened by adamnovak 7 months ago - 2 comments

#49 - Set up minimap2 hifi variant calling and evaluation control

Issue - State: closed - Opened by adamnovak 7 months ago - 2 comments

#48 - Make non-chaining codepath as fast as it used to be

Issue - State: closed - Opened by adamnovak 7 months ago - 2 comments

#47 - Fix CHM13 HiFi reads that minimap2 gets right and Giraffe gets wrong

Issue - State: open - Opened by adamnovak 7 months ago

#46 - Improve MAPQs on HiFi reads

Issue - State: open - Opened by adamnovak 7 months ago - 1 comment

#45 - Evaluate performance on centromeres that are in the graph, using CHM13 reads

Issue - State: closed - Opened by adamnovak 7 months ago - 2 comments

#44 - Get MAPQs from GraphAligner

Issue - State: closed - Opened by adamnovak 7 months ago - 1 comment

#43 - Stop surjected nanopore reads from unmapping

Issue - State: closed - Opened by adamnovak 7 months ago - 1 comment

#42 - Regression-test non-chaining short read codepath

Issue - State: closed - Opened by adamnovak 7 months ago

#41 - Evaluate mapping to centromeres using CHM13 reads

Issue - State: closed - Opened by adamnovak 7 months ago - 1 comment

#40 - Simulate CHM13 reads for evaluating centromeres

Issue - State: closed - Opened by adamnovak 7 months ago - 1 comment

#39 - Fix HiFi reads that mismap due to increased exploration of chains

Issue - State: open - Opened by adamnovak 8 months ago

#38 - Figure out and fix HiFi reads that Giraffe leaves unmapped even on the R10 preset

Issue - State: closed - Opened by adamnovak 8 months ago

#37 - Add an experiment for sampled graphs

Pull Request - State: closed - Opened by xchang1 8 months ago

#36 - Profile and optimize parameters for R10 to get good speed without reducing accuracy or increasing unaligned bases

Issue - State: closed - Opened by adamnovak 8 months ago - 1 comment

#35 - Work out why Banded Global Aligner middles are slow on Illumina reads

Issue - State: open - Opened by adamnovak 9 months ago

#34 - Work out why the fragment stage is slow on Illumina reads

Issue - State: open - Opened by adamnovak 9 months ago

#33 - Speed and memory

Pull Request - State: closed - Opened by xchang1 9 months ago

#32 - performance of vg inject

Issue - State: open - Opened by netwon123 9 months ago

#31 - Make the .W indexes actually minimizer-weighted

Issue - State: closed - Opened by adamnovak 9 months ago

#30 - Fix HiFi high MAPQ precision regression

Issue - State: closed - Opened by adamnovak 9 months ago - 1 comment

#29 - Make sure we have sufficient (~30x) coverage of real reads stored for haplotype sampling

Issue - State: closed - Opened by adamnovak 9 months ago

#28 - Change from "HiFi" sample to real HG002 HiFi reads

Issue - State: closed - Opened by adamnovak 9 months ago - 2 comments

#27 - Try one-base seed anchors

Issue - State: closed - Opened by adamnovak 9 months ago - 1 comment

#26 - Do variant calling on lr-giraffe Illumina reads and evaluate it

Issue - State: open - Opened by adamnovak 9 months ago

#25 - Debug duplicate chains in R10 reads

Issue - State: closed - Opened by adamnovak 9 months ago - 1 comment

#24 - Optimize minimizer count extra parameter

Issue - State: closed - Opened by adamnovak 9 months ago - 1 comment

#23 - Test on variant graphs from vg construct

Issue - State: closed - Opened by benedictpaten 9 months ago - 1 comment

#22 - Fix R10 softclips again

Issue - State: closed - Opened by adamnovak 9 months ago

#21 - Port paired end logic for sr code path

Issue - State: open - Opened by benedictpaten 9 months ago

#20 - Compare R9 and R10 performance with R10 preset

Issue - State: closed - Opened by adamnovak 9 months ago - 2 comments

#19 - Produce summary performance plots for R10 and Hifi

Issue - State: open - Opened by adamnovak 9 months ago

#18 - Investigate and characterize memory usage

Issue - State: closed - Opened by adamnovak 9 months ago - 1 comment

#17 - Look at R10's low relative numbers of mapQ 60 reads

Issue - State: closed - Opened by adamnovak 9 months ago - 1 comment

#16 - Optimize Q27 mapping parameters

Issue - State: closed - Opened by adamnovak 9 months ago - 1 comment

#15 - Optimize R10 mapping parameters

Issue - State: closed - Opened by adamnovak 9 months ago

#14 - Use optimal Minimap2 parameters

Issue - State: closed - Opened by adamnovak 9 months ago - 3 comments

#13 - Long read support for vg surject

Issue - State: open - Opened by adamnovak 9 months ago

#12 - Debug haplotype sampling with long read Giraffe

Issue - State: open - Opened by adamnovak 9 months ago - 2 comments

#11 - Get DeepVariant working with long read Giraffe output

Issue - State: closed - Opened by adamnovak 9 months ago

#10 - Create haplotype sampling + variant calling long read Giraffe WDL

Issue - State: closed - Opened by adamnovak 9 months ago - 2 comments

#9 - Improve WFA speed

Issue - State: closed - Opened by adamnovak 9 months ago

#8 - Re-optimize HiFi parameters using improved WFA

Issue - State: closed - Opened by adamnovak 9 months ago - 1 comment

#7 - Present long read Giraffe to HPRC call

Issue - State: closed - Opened by adamnovak 9 months ago - 1 comment

#6 - Long Read Giraffe Release

Issue - State: open - Opened by adamnovak 9 months ago

#5 - Add Q27 nanopore reads to experiment

Issue - State: closed - Opened by adamnovak 9 months ago

#4 - Re-simulate experiment reads based on current HG002 assembly

Issue - State: closed - Opened by adamnovak 9 months ago

#3 - Make paper skeleton listing figures needed

Issue - State: closed - Opened by adamnovak 9 months ago - 1 comment

#2 - Collect Illumina results

Issue - State: closed - Opened by adamnovak 9 months ago

#1 - vg versions

Pull Request - State: closed - Opened by xchang1 11 months ago

GitHub / vgteam/long-read-giraffe-experiments issues and pull requests